Rv0316 Family assigned · medium auto-curated
H37Rv Rv0316 · MTBC0 mtbc0_000336 ·
204 aa · 387858–388472 (+) ·
RefSeq NP_214830.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | muconolactone isomerase |
|---|---|
| MTBC0 PGAP re-annotation | muconolactone Delta-isomerase family protein |
| Revised (this work) | Muconolactone Delta-isomerase family protein. Pfam: MIase (PF02426.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07243
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible muconolactone isomerase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Could be involved in the catabolism of catechol to succinate- and acetyl-CoA in the beta-ketoadipate pathway (at the third step) catalytic activity 2,5-dihydro-5- oxofuran-2-acetate 3,4-dihydro-5-oxofuran-2-acetate |
| Orthologous group | COG4829 |
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.278 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
MIase | PF02426.23 | 1.0e-31 | 1–93 | Muconolactone delta-isomerase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0315 (beta-1,3-glucanase), high confidence from genomic context alone (score 843 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0315 |
beta-1,3-glucanase | 843 | 843 ctx | neighborhood:714 coexpression:474 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 535 | 535 ctx | cooccurence:535 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 528 | 528 ctx | cooccurence:528 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 528 | 528 ctx | cooccurence:528 |
Rv0314c |
membrane protein | 527 | 526 ctx | neighborhood:522 |
Rv0330c hyp |
hypothetical protein | 512 | 513 ctx | cooccurence:511 |
Rv2098c PE_PGRS36 |
PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub | 510 | 510 ctx | cooccurence:507 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 504 | 504 ctx | cooccurence:504 |
Rv3403c hyp |
hypothetical protein | 498 | 499 ctx | cooccurence:491 |
Rv2503c scoB |
succinyl-CoA:3-ketoacid-CoA transferase subunit B | 508 | 487 | coexpression:412 |
Rv1937 |
oxygenase | 692 | 485 | coexpression:410 textmining:428 |
Rv2853 PE_PGRS48 |
PE-PGRS family protein PE_PGRS48 | 473 | 473 ctx | cooccurence:473 |
Rv0867c rpfA |
resuscitation-promoting factor RpfA | 464 | 465 ctx | cooccurence:439 |
Rv2776c |
oxidoreductase | 600 | 461 | |
Rv0355c PPE8 |
PPE family protein PPE8 | 447 | 447 ctx | cooccurence:447 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: muconolactone isomerase
- MTBC0 PGAP product: muconolactone Delta-isomerase family protein
- Pfam (hmmscan --cut_ga): MIase PF02426.23 (E=1e-31)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_214830.1)
- Domains: Pfam-A via hmmscan --cut_ga — MIase (PF02426.23)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG4829 - Curated reference: UniProt O07243 (TrEMBL, unreviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
33 functional partner(s); context anchor
Rv0315 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000336|Rv0316| MEFLVTMTTRVPDSMPADAVERVRAREAARSRELAAQGKLLRLWRPPLRPGEWRTLGLFAADDNGELEQLLASMPPRSWRTDDVTPLGAHPNDPVGQGITIAPGKGPEFLIATTIMVPPGTPAQVVDDTVAREARRAPELAGRGHLVRLWALPDGPDGQRTLGLWRARDPGELMAILESLPLAGWMTIETTPLSPHPDDPIRMP